Hello,
I have some trouble with cctbx, I try to understand why and I do not succeed.
I need your help !
I replaced quartz with silicon in the "beach in the box" example/tutorial.
This is the resulting code :
from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex
silicon_structure = xray.structure(
special_position_settings=crystal.special_position_settings(
crystal_symmetry=crystal.symmetry(
unit_cell=(5.4307,5.4307,5.4307,90,90,90),
space_group_symbol="Fd3m")),
scatterers=flex.xray_scatterer([
xray.scatterer(
label="Si",
site=(0.,0.,0.),
u=0) ]))
silicon_structure.show_summary().show_scatterers()
for scatterer in silicon_structure.scatterers():
print "%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site
site_symmetry = silicon_structure.site_symmetry(scatterer.site)
print " point group type:", site_symmetry.point_group_type()
print " special position operator:", site_symmetry.special_op()
f_calc = silicon_structure.structure_factors(d_min=1).f_calc()
f_calc.show_summary().show_array()
and running the script gives the following result result :
Number of scatterers: 1
At special positions: 1
Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90)
Space group: F d -3 m :2 (No. 227)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Si Si 16 ( 0.0000 0.0000 0.0000) 1.00 0.0000
Si: 0.0000 0.0000 0.0000
point group type: -3m
special position operator: 0,0,0
Miller array info: None
Observation type: None
Type of data: complex_double, size=9
Type of sigmas: None
Number of Miller indices: 9
Anomalous flag: False
Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90)
Space group: F d -3 m :2 (No. 227)
(0, 2, 2) 0j
(0, 4, 0) (120.217658126+0j)
(1, 1, 1) (-84.1884955081+0j)
(1, 3, 1) (65.4837172721+0j)
(1, 3, 3) (57.4543830832+0j)
(1, 5, 1) (-51.4875968695+0j)
(2, 2, 2) (128.545406989+0j)
(2, 4, 2) 0j
(3, 3, 3) (-51.4875968695+0j)
The 220 structure factor, at least, does not look correct . I do not
understand the 16 multiplicity either. Is there something I miss ?
Best regards
Marc
